title: pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.
abstract: Shifting of pKa's in RNA is important for many biological processes; however, the driving forces responsible for shifting are not well understood. Herein, we determine how structural environments surrounding protonated bases affect pKa shifting in double-stranded RNA (dsRNA). Using (31)P NMR, we determined the pKa of the adenine in an A(+)·C base pair in various sequence and structural environments. We found a significant dependence of pKa on the base pairing strength of nearest neighbors and the location of a nearby bulge. Increasing nearest neighbor base pairing strength shifted the pKa of the adenine in an A(+)·C base pair higher by an additional 1.6 pKa units, from 6.5 to 8.1, which is well above neutrality. The addition of a bulge two base pairs away from a protonated A(+)·C base pair shifted the pKa by only ~0.5 units less than a perfectly base paired hairpin; however, positioning the bulge just one base pair away from the A(+)·C base pair prohibited formation of the protonated base pair as well as several flanking base pairs. Comparison of data collected at 25 °C and 100 mM KCl to biological temperature and Mg(2+) concentration revealed only slight pKa changes, suggesting that similar sequence contexts in biological systems have the potential to be protonated at biological pH. We present a general model to aid in the determination of the roles protonated bases may play in various dsRNA-mediated processes including ADAR editing, miRNA processing, programmed ribosomal frameshifting, and general acid-base catalysis in ribozymes.
authors.affiliation: Department of Chemistry and Center for RNA Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Wilcox
authors.forename: Philip C
authors.initials: PC
authors.lastname: Bevilacqua
mesh_terms: D000225:Adenine / Q000737:chemistry*; D020029:Base Pairing; D006863:Hydrogen-Ion Concentration; D008274:Magnesium / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012330:RNA, Double-Stranded; D008274:Magnesium; D000225:Adenine